St. Thomas one of the twelve apostles of Jesus Christ came to Malankara (Kerala) and established Kottakadav (N.Paravur) Church in A.D.58, which is one among the oldest church in Malankara. For their convenience, few Christians from the southern part of Ernakulum established a new church in Edapally . The people from Malayidomthuruth , Kizakkambalam , Vengola, Thamarachal , Oorakkad , Pallikkara use to attend the holy service at St. George Syrian church Edapally.
Twenty years after the Nicean Council (synod), Knai Thoma, a rich international merchant from Cana, brought a colony of 400 Syrian Christians consisting of 72 families belonging to 7 clans with instructions from the Patriarch of Antioch, Mor Yusthedius, to the Malabar coast of India. Mor Joseph and Knai Thoma landed in Kodungalloor (Crangannoore) in 345 AD. Knai Thoma and his people were heartily welcomed by Cheraman Perumal, the Emperor. Cheraman Perumal sent his brother, Ramavarma, and his minister, Vettathu Mannan, to receive Knai Thoma and his people. Knai Thoma and his people were given permission to settle down in Kodungalloor and to do business. Later Cheraman Perumal bestowed Knai Thoma and his people with 72 princely privileges and there by elevated them over 17 castes. This proclamation was made on a Saturday in March (Kumbham 29), 345 and it was recorded on copper plates given to Knai Thoma (Knai Thomman Cheppedu). Knai Thoma and his people built a town in Kodungalloor with a church and 72 house
Due to lack of availability of transportation to reach Edapally church, people living in and around pallikara , malayidomthuruth and Kizakkambalam establish a new church in Pallikara in AD 905. Records kept in the church bear out details that the delegates from St. Mary’s Syrian church Pallikkara attended the historic “Koonan Kurishu Sathyam” in 1653.
The dark period of malankara church was during the rule of malankara metropolitan Vattasseril Mor Dionysius. In 1911 May 21, H. H. Moran Mar Ignatius Abdullah Patriarch came over to Malankara and excommunicated Vattasseril Mor Dianysius. This caused a rift in the malankara church. Due to this two factions were formed. One group which supported Patriarch of Antioch were called Jacobite Syrian Church(Bawa-kashi) and the others known as Indian Orthodox faction (Metharan-kakshi).
In 1914 people around Oorakkad , Malayidomthuruth , Ambunadu and Karukulam decided to build a new church at Oorakad in the name of St. Thomas under the Holy See of Antioch and all the east. Christians around malayidomthuruth performed their religious rites in St. Thomas Jacobite Syrian Orthodox Church Oorakkad which is 5 KM away from Malayidomthuruth. There were no proper roads or transportation available at that point in time from malayidomthuruth to Oorkad and they also faced other difficulties if they wanted to attend the Holy Qurbaono regularly and to perform their religious rites. Hence they decided to have a church of their own in Malayidomthuruth. The general body held on 17.1.1975 at St. Thomas church Orrakkad approved the request of people from malayidomthuruth and agreed to declare St. George chapel at malayidomthuruth as Malayidomthuruth Church.
It was a historic moment for the people of malayidomthurth, on 18th of January 1975 Rev. Father P.K Mathai celebrated the first Holy Qurbaono at St. George Jacobite Syrian Orthodox Church Malayidomthurth. On 19th of January 1975 the first general body chaired by Sri. C.C Vargehse at the church which includes all Syrian Christian at malayidomthurth (those were attending services at St.Thomas Church Oorakkad , St. Mary’s Church Thamarachal and St.George Church Vazakulam) decided to buy land for the new church in malayidomthuruth. On 8th February 1975 metropolitan of Angamli dioceses H.E Mor Dionysius Thomas called for a general body and affirmed that the three altars in the church are dedicated to Holy Virgin Mary (Main altar) , St. Thomas the Apostle and St. George the Martyr (Mor Geevarghese Sahdo).
Their grace H. E. Mor Osthateus Thomas (Auxiliary bishop) of Kandanad dioceses consecrated the temporary church on September 14th 1975. On October 1st 1975 H.E Mor Dionysius Thomas bishop of Angamli dioceses appointed Rev. Father E.C Varghese as the Vicar of St. Mary’s Church Malayidomthuruth. By the grace of God and on the admirable leadership of Rev. Father E.C Varghese we were able to complete the construction on time . On 14th September 1976 Metropolitan of Angamli dioceses H.E Mor Dionysius Thomas consecrated the St. Mary’s Jacobite Syrian Orthodox Church Malayidomthuruth and celebrate the first Holy tri-Qurbaono . The General body conducted on 26th of December 1976 decided to celebrate the main feast of the church on 8th of September every year. At the beginning of the church there were 113 families, now there are more than 250 families, 2 chapels and 4 shrines under malayidomthuruth church.